A difficult decision faced Futaba, Japan this January. The vacant town, located within the Prohibited Zone created after the Fukushima nuclear leak in 2011 (which continues to spill toxic effluent into the Pacific Ocean), was asked to host a radioactive materials storage facility, for the bags of radioactive topsoil and debris that have been sitting in fields around the area for years. The exiled municipal authorities agreed – perhaps sealing the fate of the city even should it be cleared one day for repopulation.

Despite the promise that the stuff will be taken away within 30 years, temporary has a way of blending into permanence. Meanwhile, 120,000 residents of Fukushima Prefecture remain evacuated – a reminder that while ionised radiation is a fact of life for us all, for residents of some cities it’s a daily source of worry.

It’s not always easy to know how radioactive your city is, though – or at least how dangerous the radiation makes it. The amount of radioactive material in the environment is not the only factor: many of the bioactive effects don’t stem from direct radiation but rather from that radioactive material’s access to your body, in the air you breathe or the plants you eat.

Aberdeen in Scotland, for example, is founded on radium-rich rock, and is often called a “radioactive city”. But without fissures in that rock for radon to escape, the dangerous gas remains trapped and harmless. Were the city located just a few kilometres further north, where cracks in the bedrock are abundant, it would be a different story: significant work might need to go into ground-floor ventilation.

Radon gas is the second-biggest contributor to lung cancer, and its effects are enhanced by the leading cause, smoking. On the coast of the Caspian Sea, the city of Ramsar, Iran has such high natural background radiation levels that scientists have recommended that the 32,000 residents relocate. Its neighbourhood of Talesh Mahalleh, the most naturally radioactive inhabited area in the world, is under long-term study.

Aberdeen is often called a 'radioactive city', but the dangerous gas is trapped in the bedrock

The houses in Ramsar are partly to blame. Uranium-rich igneous rock is dissolved by groundwater that emerges to the surface in nine hot springs (which are used for bathing). There, the radium enters into the limestone from which most of the local houses are built. It also infuses the drinking water and accumulates in the crops.

Is it dangerous, though? Lung cancer rates are no higher than average in Ramsar, although small population sizes don’t warrant a statistically significant claim. Given that 40% of us will develop cancer during our lifetime, the causes of small-town “cancer clusters” are hard to pin on local factors, rather than on bad luck.

Statistical ambiguity also dogs Tularosa, New Mexico, which stands 35 miles from the Trinity nuclear weapons testing site in Nevada. It was here, on 16 July 1945 – just weeks before the bombing of Hiroshima – that the US military conducted a test run of nuclear explosions, coating the backyards of Tularosa homes with ash. The residents struggled to prove the ill effects of the fallout, however, and years of court battles followed. Finally, in 1990 the US Congress lifted the burden of proof for Tularosa victims and offered $50,000 compensation to any downwind residents who contracted certain cancers.

An ostrich escaped from a farm walks past a car within the exclusion zone around Fukushima. Photograph: Issei Kato/Reuters

One of the difficulties is that there are a dozen ways to measure the severity of ionising radiation. The two SI units are the Gray (Gy), which indicates an actual dose received, and a Sievert (Sv), which is the dose equivalent, a joule of energy per kilogram. The residents of Talesh Mahalleh, for example, receive an average dose of 10 mGy per year – 10 times the International Commission on Radiological Protection’s recommended limit from artificial sources. One house clocked in at 131 mSv per year, or more than 80 times the world average. In theory, one Sievert confers a 5.5% increased probability of cancer. Effects are more severe for fetuses and children, and are much milder for the elderly – unless that one Sievert is delivered over a very short timespan, in which case radiation poisoning leads to death within days for anyone.

The missing factor is human behaviour. For instance, gold mining in South Africa’s Witwatersrand Basin – on which Johannesburg’s economy was founded – has left 120 mines’ worth of pyrite tailings, containing 450,000 tonnes of uranium. Torrential rainfall, probably due to climate change, has flooded those ponds and underground stockpiles, flushing radioisotopes into the groundwater. This would clearly be a problem if Jo’burg residents were drinking local water – but the city buys its supplies from Rand Water, which extracts it from the Vaal river, 80km away.

Or take Slavutych, a Ukranian city about 50km east of the Chernobyl nuclear power plant. Slavutych was built specifically to house the displaced residents of Pripyat, the famous abandoned city that now lies within an exclusion zone the size of Lancashire. And yet until the shutdown of the last active reactor at Chernobyl in 2001, staff still worked there, commuting directly from Slavutych train station. Residents are also employed as guards around the exclusion zone – one of the most contaminated places on Earth and also, bizarrely, one of the largest nature preserves in Europe, home to lynx, bison, wolves and brown bears. To make matters worse, 8,000 of Slavutych’s residents were children at the time of the 1986 meltdown.

Many bioactive effects stem from radioactive materials in the air, water and food. Photograph: Majid/Getty

Radiation-related illnesses and thyroid abnormalities are common in Slavutych (though it’s important to keep the danger in perspective: suicide is a 20-fold higher risk for young people in Slavutych than thyroid cancer). How much radiation the people receive depends on the extent to which they eat locally grown food. Surface-level radiation exposure has become less severe over time in the Chernobyl area, but radioactive caesium permeates deeper in the soil. Mushrooms, in particular, are severely contaminated, because they concentrate heavy metals in their tissues. Still, denial prevails, misinformation abounds (vodka is understood by many to cleanse the body of radioactivity), and many residents eat local produce with blithe confidence.

In Slavutych, near Chernobyl, vodka is still understood by many to cleanse the body of radioactivity

Chernobyl remains the worst nuclear power plant accident in history. Recency compounds severity, however, and Fukushima is currently in worse straits. Much of the radioactive material was borne out to sea by wind or waves, but the rest was dispersed in a populated area to the northwest of the plant. Residents of the city of Tomioka have been allowed home, but so far only during the day – and around 40% of them have decided never to return.

To see the city, you wouldn’t think it had been fully inhabited as recently as four years ago. Wild boar have interbred with farm pigs and rampaged through the town, with no experience – or fear – of humans. The buildings are crumbling and rats are thriving. The isotopes of concern are iodine-131, which accumulates in and irradiates the thyroid gland for weeks after exposure (but has by now faded in Tomioka), and caesium-137, which permeates Tomioka’s topsoil to a depth of five or more centimetres. Hence the effort to bag up that layer of earth – particularly in playgrounds – for storage in Futaba.

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How radioactive is Tomioka? As always, it’s hard to say for certain. Here’s the author William T Vollman on a visit in 2013: “Right by the pachinko parlour [the] scintillation counter read 4.2 microsieverts per hour — about 10 times the level of that mildly dangerous drainpipe in Hisanohama. At a nearby house with yellow danger tape around it, the base of a drainpipe registered 22.1 microsieverts per hour. The daily dose would be 530.4 microsieverts; the yearly dose, 193.6 millisieverts. A little perilous, I’d say. The grassy field was a cool 7.5 microsieverts per hour — 65.7 millisieverts per year — while the main highway on which the decontamination trucks kept raising dust was only 3.72 per hour, which still comes to 32 times the recommended annual dose.”

Not surprisingly, farmers near the city had to scrap the first year of crops after the disaster, and slash prices on the second. Fisheries have been decimated. Even as the radiation levels above ground stabilise, the legacy for Tomioka and Fukushima Prefecture in general will be a long one, as caesium seeps deeper into the ground on its slow journey to the groundwater. It may be a dubious honour among inhabited cities, but for this year at least, Tomioka is the world’s most radioactive.

• This article was amended on 15 May 2015 to clarify that a Sievert (Sv) is the dose equivalent, a joule of energy per kilogram, rather than “the dose a human in that environment would be expected to receive”. It also corrected “ionised” radiation to “ionising”.